Programming a topologically constrained DNA nanostructure into a sensor

Nat Commun. 2016 Jun 23;7:12074. doi: 10.1038/ncomms12074.


Many rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml(-1), thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosensing Techniques*
  • DNA, Bacterial
  • DNA, Catenated / chemistry*
  • Escherichia coli K12
  • Nanostructures*
  • Nucleic Acid Amplification Techniques / methods*


  • DNA, Bacterial
  • DNA, Catenated